REFER TO SEGMENT
Proper referencing of Segment when publishing scientific results is a prerequisite for using Segment. This is vital. We are dependent on proper citations in order to continue to release the software freely available for researchers.
Please see the list of researchers who has already remembered to give us credit by a proper citation.
A reference should encompass both the name Segment, and a suitable publication. When in doubt, please send an email to email@example.com or put reference  which is the generic reference for image analysis in Segment. This open-access paper describes Segment and its potential uses.
Examples of possible formulations for references
Note that referencing the software is manditory also for abstracts to scientific conferences. If shortage of space, at least reference the software as something like:
Images was analysed using the freely available software Segment (http://segment.heiberg.se).
In extreme shortage of space, such as conferences where the word limit is less than 350 words then reference may be omitted in the abstract text, but should be included in the oral presentation and / or poster.
Using the new automatic LV segmentation in the software (version later than v2.0 R4265) should be referenced by . Using the old semi automatic LV segmentation in the software (version earlier than v1.9 R4245) should be referenced by . Using the software for manual segmentation of the LV should be referenced by .
 J. Tufvesson, E. Hedstrom, K. Steding-Ehrenborg, M. Carlsson, H. Arheden, and E. Heiberg, Validation and Development of a New Automatic Algorithm for Time-Resolved Segmentation of the Left Ventricle in Magnetic Resonance Imaging, Biomed Res Int, 2015:970357.
 E. Heiberg, L. Wigström, M. Carlsson, A.F. Bolger, M. Karlsson, Time Resolved Three-dimensional Segmentation of the Left Ventricle, In proceedings of IEEE Computers In Cardiology 2005(32), pp. 599-602, Lyon, France, 2005.
The current algorithm for infarct quantification is EWA and should be referenced as . The old weighted version should be referenced as . Measurement of endocardial extent should be referenced to as . Gray zone analysis should be referenced as gray zone analysis using weighted method using either  or  as reference. If the ROI based gray zone algorithm is used then the algorithm should be referred to as .
 H. Engblom, J. Tufvesson, R. Jablonowski, M. Carlsson, A. H. Aletras, P. Hoffmann, A. Jacquier, F. Kober, B. Metzler, D. Erlinge, D. Atar, H. Arheden, and E. Heiberg, A new automatic algorithm for quantification of myocardial infarction imaged by late gadolinium enhancement cardiovascular magnetic resonance: experimental validation and comparison to expert delineations in multi-center, multi-vendor patient data, J Cardiovasc Magn Reson 18(1) p 27, 2016.
 E. Heiberg, M. Ugander, H. Engblom, M. Götberg, G. K. Olivecrona, D. Erlinge, and H. Arheden, Automated quantification of myocardial infarction from MR images by accounting for partial volume effects: animal, phantom, and human study, Radiology 246(2) pp. 581-8, 2008.
 H. Engblom, M. B. Carlsson, E. Hedstrom, E. Heiberg, M. Ugander, G. S. Wagner, and H. Arheden, The endocardial extent of reperfused first-time myocardial infarction is more predictive of pathologic Q waves than is infarct transmurality: a magnetic resonance imaging study, Clin Physiol Funct Imaging 27(2) pp. 101-8, 2007.
 Wu KC, Gerstenblith G, Guallar E, Marine JE, Dalal D, Cheng A, Marbán E, Lima JAC, Tomaselli GF, Weiss RG. Combined cardiac MRI and C-reactive protein levels identify a cohort at low risk for defibrillator firings and death. Circ Cardiovasc Imaging 2012; 5:178-86. PMCID:PMC3330427
Using the new vessel tracking algorithm in the software (version later than v2.0 R4579) should be referenced by . Using the old vessel tracking algorithm in the software (version earlier than v2.0 R4534) should be referenced by .
 S. Bidhult, M. Carlsson, K. Steding-Ehrenborg, H. Arheden, and E. Heiberg, A new method for vessel segmentation based on a priori input from medical expertise in cine phase-contrast Magnetic Resonance Imaging. In Proceedings of Seventeenth Annual SCMR Scientific Sessions, New Orleans, USA, 2014.
 E. Heiberg, K. Markenroth, and H. Arheden Validation of free software for automated vessel delineation and MRI flow analysis. In Proceedings of Tenth Annual SCMR Scientific Sessions, Rome, Italy, 2007.
Strain analysis module
The strain analysis module includes both feature tracking and tagging analysis. The underlying algorithms for the strain tracking are given in  or . The clinical reproducibility of feature tracking in cineMRI is reported in .
 B. Heyde, R. Jasaityte, D. Barbosa, V. Robesyn, S. Bouchez, P. Wouters, F. Maes, P. Claus, J. D’hooge. Elastic image registration versus speckle tracking for 2-D myocardial motion estimation: a direct comparison in vivo. IEEE Trans Med Imaging. 2013 Feb;32(2):449-459.
 P. Morais, B. Heyde, D. Barbosa, S. Queirós, P. Claus, and J. D’hooge. Cardiac motion and deformation estimation from tagged MRI sequences using a temporal coherent image registration framework. Proceedings of the meeting on Functional Imaging and Modelling of the Heart (FIMH), Lecture Notes in Computer Science, vol. 7945, pages 316-324, London, 2013.
 P. Morais, A. Marchi, JA. Bogaert, T. Dresselaers, B. Heyde, J. D’hooge, J. Bogaert. Cardiovascular magnetic resonance myocardial feature tracking using a non-rigid, elastic image registration algorithm: assessment of variability in a real-life clinical setting. J Cardiovasc Magn Reson 2017 Feb 17;19(1):24.
Myocardium at Risk
Segmentation of myocardium at risk from T2 STIR imaging should be referred to as . Segmentation of myocardium at risk from CE-SSFP should be referenced to as .
 J. Sjogren, J. F. Ubachs, H. Engblom, M. Carlsson, H. Arheden, and E. Heiberg, Semi-automatic segmentation of myocardium at risk in T2-weighted cardiovascular magnetic resonance, J Cardiovasc Magn Reson 14(1) p 10, 2012.
 J. Tufvesson, M. Carlsson, A. H. Aletras, H. Engblom, J. F. Deux, S. Koul, P. Sorensson, J. Pernow, D. Atar, D. Erlinge, H. Arheden, and E. Heiberg, Automatic segmentation of myocardium at risk from contrast enhanced SSFP CMR: validation against expert readers and SPECT, BMC Med Imaging 16 p 19, 2016.
Bulls eye analysis
Creating and exporting bulls eyes plots should be referenced to as .
 P. A. Cain, M. Ugander, J. Palmer, M. Carlsson, E. Heiberg, and H. Arheden, Quantitative polar representation of left ventricular myocardial perfusion, function and viability using SPECT and cardiac magnetic resonance: initial results, Clin Physiol Funct Imaging 25(4) pp. 215-22, 2005.
Creating T2* maps and analysis should be referenced to as . Creating T1, or T2 maps and analysis should be referenced as .
 S. Bidhult, C. G. Xanthis, L. L. Liljekvist, G. Greil, E. Nagel, A. H. Aletras, E. Heiberg, E. Hedström, Validation of a New T2* Algorithm and Its Uncertainty Value for Cardiac and Liver Iron Load Determination from MRI Magnitude Images. Magn Reson Med, May 22, 2015.
 S. Bidhult, G. Kantasis, A. H. Aletras, H. Arheden, E. Heiberg, and E. Hedstrom, Validation of T1 and T2 algorithms for quantitative MRI: performance by a vendor-independent software, BMC Med Imaging 16(1) p 46, 2016.
Pulse wave velocity
Usage of the pulse wave velocity should be referenced as .
 K. Dorniak, E. Heiberg, M. Hellmann, D. Rawicz-Zegrzda, M. Wesierska, R. Galaska, A. Sabisz, E. Szurowska, M. Dudziak, and E. Hedstrom, Required temporal resolution for accurate thoracic aortic pulse wave velocity measurements by phase-contrast magnetic resonance imaging and comparison with clinical standard applanation tonometry, BMC Cardiovasc Disord 16(1) p 110, 2016.
Usage of the Fusion Module should be referenced with reference .
 M. Ugander, H. Soneson, H. Engblom, J. v. d. Pals, D. Erlinge, E. Heiberg, and H. Arheden, Semi-automatic quantification of myocardium at risk in myocardial perfusion SPECT by co-registration and fusion with delayed contrast enhanced MR imaging – an experimental ex vivo study, Clin Physiol Func Imag, 32(1) pp 33-38, 2012.
Myocardial perfusion SPECT analysis
Quantification of LV mass in SPECT images should be referenced to with reference . Quantification myocardium at risk in SPECT images should be referenced to with reference . Quantification of LV volumes in SPECT images should be referenced to with reference . Quantification of ischemia in SPECT images should be referenced to with reference .
 H. Soneson, J. F. Ubachs, M. Ugander, H. Arheden, and E. Heiberg, An Improved Method for Automatic Segmentation of the Left Ventricle in Myocardial Perfusion SPECT, J Nucl Med 50(2) pp. 205-13, 2009.
 H. Soneson, H. Engblom, E. Hedstrom, F. Bouvier, P. Sorensson, J. Pernow, H. Arheden, and E. Heiberg, An automatic method for quantification of myocardium at risk from myocardial perfusion SPECT in patients with acute coronary occlusion, J Nucl Cardiol 17(5) pp. 831-40, 2010.
 H. Soneson, F. Hedeer, C. Arevalo, M. Carlsson, H. Engblom, J. F. Ubachs, H. Arheden, and E. Heiberg, Development and validation of a new automatic algorithm for quantification of left ventricular volumes and function in gated myocardial perfusion SPECT using cardiac magnetic resonance as reference standard, J Nucl Cardiol, 2011.
 H. Fransson, M. Ljungberg, M. Carlsson, H. Engblom, H. Arheden, and E. Heiberg, Validation of an automated method to quantify stress-induced ischemia and infarction in rest-stress myocardial perfusion SPECT, J Nucl Cardiol, 21(3) pp 503-18 2014.